A file photo of the headquarters of the Organization for the Prohibition of Chemical Weapons (OPCW) in The Hague. (AFP Photo)
United Nations secretary general Ban Ki-moon welcomed the news on Monday and said the successful completion of such a tricky exercise showed that, when there was the political will, "there can be progress towards peace".
Speaking in New York, he praised several countries for their role, including China, Russia, Britain and the United States as well as Syria itself.
"As we speak, the ship (carrying the last chemicals) has just left the port (of Latakia)," Ahmet Uzumcu, head of the Organisation for the Prohibition of Chemical Weapons, told journalists Monday in The Hague, where the OPCW is based.
"Removing the stockpile of precursor and other chemicals has been a fundamental condition in the programme to eliminate Syria's chemical weapons," Uzumcu said.
The Dutch head of the joint OPCW-UN mission, Sigrid Kaag, hailed the end of "the most operationally challenging task" in the international efforts to destroy Damascus' chemical arsenal.
Syria had previously shipped out 92 percent of its stockpile of chemical weapons under the terms of a UN-backed and US-Russia brokered agreement to head off Western air strikes against the regime last year.
But Damascus delayed shipping the remaining eight percent of the stockpile from another site, citing security concerns over transporting it to the port of Latakia.
"While a major chapter in our endeavours closes today, OPCW's work in Syria will continue," Uzumcu said.
"We hope to conclude soon the clarification of certain aspects of the Syrian declaration and commence the destruction of certain structures that were used as chemical-weapons production facilities."
The Syrian foreign ministry confirmed in a statement that "the final cargo of chemical agents has today been taken outside Syrian territory".
The ministry hailed the success of the mission and called on the international community to pressure Syria's arch-foe Israel to sign up to international agreements on weapons of mass destruction.
Russia's foreign minister, meanwhile, voiced "deep satisfaction" at what it hailed as "the successful end of a large-scale and unprecedented international operation".
Kaag said technical experts from The Hague, the joint mission and the Syrian authorities would continue to investigate "the completeness of Syria's initial declaration to the OPCW".
"The most important thing is that the materials are out. They will be destroyed safely and securely... out of harm's way, and they can also no longer fall into the wrong hands," Kaag told AFP.
Syria was supposed to hand over its chemical arsenal so the international community could destroy it by the end of June, but it has been widely acknowledged it would pass that deadline.
"While the June 30 deadline, as already was stated a few weeks ago, will not be met... the materials are out of the country and the bulk of Syria's declared chemical weapons programme is no more," said Kaag.
The deal was reached after the US threatened to carry out air strikes against President Bashar al-Assad's regime following a sarin nerve gas attack in a rebel-held suburb in Damascus last year that killed around 1,400 people.
A Danish ship will now take the chemicals to Italy's port of Gioia Tauro, where they will be transferred to the US ship Cape Ray for destruction at sea. Some are also due to be destroyed in the US, Britain and Finland.
OPCW spokesman Michael Luhan told AFP that the Danish vessel would arrive in Italy "within a week". Uzumcu confirmed that once they have been transferred to the US vessel it could take up to 60 days to destroy them.
"Within the next four months most chemicals will be destroyed," he said, adding that Damascus' cooperation has been "commensurate with the requirements" of the deal.
His words contrast with news from an OPCW investigation team, which last week said chemical agents such as chlorine, which Syria was not obliged to hand over, have recently been used "in a systematic manner in a number of attacks".
Assad's regime and the rebels have both accused the other of using chemical agents in the bloody uprising that began in March 2011.
The OPCW team was attacked on May 27 while probing an alleged chlorine attack, but managed to obtain evidence the chemical had been used as a weapon.
France and the US have also alleged that Assad's forces unleashed industrial chemicals on several rebel-held villages in recent months.
Syria did not have to declare its stockpile of chlorine -- a weak toxic agent that can be turned into a weapon -- under the disarmament deal as it is widely used for commercial and domestic purposes.